biomart                 Main BioMart Query Function
biomartr-package        Genomic Data Retrieval
cachedir                Get directory to store back end files like
                        kingdom summaries etc
cachedir_set            Set directory to store back end files like
                        kingdom summaries etc
check_annotation_biomartr
                        Check whether an annotation file contains
                        outlier lines
download.database       Download a NCBI Database to Your Local Hard
                        Drive
download.database.all   Download all elements of an NCBI databse
ensembl_divisions       List all available ENSEMBL divisions
get.ensembl.info        Helper function to retrieve species information
                        from the ENSEMBL API
getAssemblyStats        Genome Assembly Stats Retrieval
getAttributes           Retrieve All Available Attributes for a
                        Specific Dataset
getBio                  A wrapper to all bio getters, selected with
                        'type' argument
getBioSet               Generic Bio data set extractor
getCDS                  Coding Sequence Retrieval
getCDSSet               CDS retrieval of multiple species
getCollection           Retrieve a Collection: Genome, Proteome, CDS,
                        RNA, GFF, Repeat Masker, AssemblyStats
getCollectionSet        Retrieve a Collection: Genome, Proteome, CDS,
                        RNA, GFF, Repeat Masker, AssemblyStats of
                        multiple species
getDatasets             Retrieve All Available Datasets for a BioMart
                        Database
getENSEMBL              Download sequence or annotation from ENSEMBL
getENSEMBL.Seq          Helper function for retrieving biological
                        sequence files from ENSEMBL
getENSEMBL.gtf          Helper function for retrieving gtf files from
                        ENSEMBL
getENSEMBLGENOMESInfo   Retrieve ENSEMBLGENOMES info file
getENSEMBLInfo          Retrieve ENSEMBL info file
getFilters              Retrieve All Available Filters for a Specific
                        Dataset
getGENOMEREPORT         Retrieve NCBI GENOME_REPORTS file
getGFF                  Genome Annotation Retrieval (GFF3)
getGFFSet               GFF retrieval of multiple species
getGO                   Gene Ontology Query
getGTF                  Genome Annotation Retrieval (GTF)
getGenome               Genome Retrieval
getGenomeSet            Genome Retrieval of multiple species
getGroups               Retrieve available groups for a kingdom of life
                        (only available for NCBI RefSeq and NCBI
                        Genbank)
getKingdomAssemblySummary
                        Retrieve and summarise the assembly_summary.txt
                        files from NCBI for all kingdoms
getKingdoms             Retrieve available kingdoms of life
getMarts                Retrieve information about available Ensembl
                        Biomart databases
getMetaGenomeAnnotations
                        Retrieve annotation *.gff files for metagenomes
                        from NCBI Genbank
getMetaGenomeSummary    Retrieve the assembly_summary.txt file from
                        NCBI genbank metagenomes
getMetaGenomes          Retrieve metagenomes from NCBI Genbank
getProteome             Proteome Retrieval
getProteomeSet          Proteome retrieval of multiple species
getRNA                  RNA Sequence Retrieval
getRNASet               RNA Retrieval of multiple species
getReleases             Retrieve available database releases or
                        versions of ENSEMBL
getRepeatMasker         Repeat Masker Retrieval
getSummaryFile          Helper function to retrieve the
                        assembly_summary.txt file from NCBI
getUniProtInfo          Get uniprot info from organism
getUniProtSTATS         Retrieve UniProt Database Information File
                        (STATS)
is.genome.available     Check Genome Availability
listDatabases           Retrieve a List of Available NCBI Databases for
                        Download
listGenomes             List All Available Genomes either by kingdom,
                        group, or subgroup
listGroups              List number of available genomes in each
                        taxonomic group
listKingdoms            List number of available genomes in each
                        kingdom of life
listMetaGenomes         List available metagenomes on NCBI Genbank
meta.retrieval          Perform Meta-Genome Retrieval
meta.retrieval.all      Perform Meta-Genome Retrieval of all organisms
                        in all kingdoms of life
organismAttributes      Retrieve Ensembl Biomart attributes for a query
                        organism
organismBM              Retrieve Ensembl Biomart marts and datasets for
                        a query organism
organismFilters         Retrieve Ensembl Biomart filters for a query
                        organism
read_assemblystats      Import Genome Assembly Stats File
read_cds                Import CDS as Biostrings or data.table object
read_genome             Import Genome Assembly as Biostrings or
                        data.table object
read_gff                Import GFF File
read_proteome           Import Proteome as Biostrings or data.table
                        object
read_rm                 Import Repeat Masker output file
read_rna                Import RNA as Biostrings or data.table object
refseqOrganisms         Retrieve All Organism Names Stored on refseq
summary_cds             Retrieve summary statistics for a coding
                        sequence (CDS) file
summary_genome          Retrieve summary statistics for a genome
                        assembly file
